Can you edit your question to include the commands you are using to zip and unzip the files?
– BurgiMay 1 '16 at 14:53

Ugh. I loathe the terminology being used here. You don't zip files with gzip. You gzip files with gzip. If you're zipping files, you do so with a command such as the "zip" command (which typically refers to Info-Zip), or maybe another command (like 7za). gzip only handles one file per .gz archive. The workaround to that limitation is to use another format to archive multiple files and then have gzip compress that archive. In Unix (I note that this question has the Unix tag), the most traditional format to use for that task is tar.
– TOOGAMMay 1 '16 at 15:36